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Biodiversity Literature after Disentis: FAIR, AI-assisted, XML-First Publishing Workflows
No full textFor over a decade, a lot of effort has been put into making millions of pages and taxonomic treatments available online. Yet, too often, biodiversity knowledge remains locked in hardly accessible and non-machine-readable literature and electronic resources. Indeed, most prospective publications are still produced in an “old-fashioned” way (PDF), thereby posing a risk of following a pattern we have seen with legacy literature from the past centuries.Even though access barriers can be demolished using retroconversion (i.e., converting a PDF into an XML annotated file once the article is published), it is far more efficient to have author- and editor-vetted annotations and semantic enhancements to the texts and data ready ahead of publication. Doing so avoids discrepancies, and ensures earlier and rapid dissemination and re-use of data. Beyond open access, the challenge for publishers is to reach interoperability, which would ultimately shorten the too-long time to find and analyse past literature (Fontaine et al. 2012) and therefore speed up the description of taxonomy.Making data within publications findable, accessible, interoperable, and reusable (FAIR) implies text structuration, semantic annotations*1, and standardization. Furthermore, to link data, information and knowledge contained in literature and other electronic resources to uniquely identifiable components (i.e., images, tables, references, taxonomic treatments; see Fig. 1) means that those would be re-usable in research and policy covering biodiversity and other domains. Ultimately, this enables immediate re-use of the data, and the integration of publications into a comprehensive global biodiversity knowledge graph.Following the vision of the Disentis roadmap*2, this presentation will outline and demonstrate the value of advanced methods for scholarly publishing, production and FAIRisation of biodiversity data during the journal production process. We described the latest developments in the scientific publishing industry and—more specifically—how to publish linked and semantically enhanced research outcomes. The presentation clarifies the concepts that are relevant within the publication for semantic enhancement. Highly-automated, XML-first, AI-assisted existing workflows for semantic enhancement of articles are introduced, including the related standards, all dedicated to making published data FAIR by creating bi-directional linked data from and to the published article. Semantization goes beyond metadata and all relevant information for biodiversity are isolated, annotated, and linked with persistent identifiers (Chester et al. 2019, Agosti et al. 2022) including: taxonomic treatment, taxon names, material examined, and material citation, the latter including country, locality, coordinates, collection date, collectors, and specimen code.Once annotated, the XML-based publication can be disseminated through a partnership with Plazi and all components pushed to relevant databases, e.g., Ocellus, Global Biodiversity Information Facility (GBIF), Biodiversity PMC (PubMed Central), ChecklistBank, National Center for Biotechnology Information (NCBI). The potential reuse of data is multiple and will benefit the publishers as well as the research community. Indeed, this wide dissemination of data contained within their articles enables publishers to create dashboards to measure e.g., numbers of articles published, numbers for data described, the richness of the data, the number of occurrences by continent.The benefits are multiple: not only do XML-first journal production workflows save time, effort and provide FAIR-born data on the day of publication, they optimize and accelerate the dissemination of data while providing human- and machine-readable publications. Semantically structured FAIR data pave the way for training and use of AI in publishing
Morphological and phylogenetic analyses reveal one new genus and six new species in Irpicaceae and Steccherinaceae (Polyporales, Basidiomycota) from the Yunnan–Guizhou Plateau, Asia
No full textPolyporales is a diverse group of Agaricomycetes that has received extensive attention and study. Species in Irpicaceae and Steccherinaceae (Polyporales) are important wood-decaying fungi that cause white rot on both angiosperm and gymnosperm wood. Recently, many studies have focused on the classification of Irpicaceae and Steccherinaceae, but the familial placements of some taxa remain unresolved. In the present study, phylogenies of species in the two families were reconstructed using multilocus DNA sequence data, including ITS, nLSU, mtSSU, tef1-α, and rpb2, as well as two combined datasets: ITS+nLSU+mtSSU+rpb2+tef1-α for Steccherinaceae and ITS+nLSU for Efibula and related species. Three new species of Efibula, one new species of Phanericium within the family Irpicaceae, and one new genus, Odentinium, including two new species, O. aurantium and O. cremeum, within the family Steccherinaceae, are described and illustrated. The genus Odentinium is characterized by resupinate basidiomata with an odontioid hymenial surface, a monomitic hyphal system with clamped generative hyphae, cylindrical cystidia that are strongly encrusted, and ellipsoid, smooth basidiospores. Furthermore, the evolutionary times of Polyporales, including Irpicaceae and Steccherinaceae, were inferred based on conserved regions of DNA sequences (ITS+nLSU+mtSSU+rpb2+tef1-α). Bayesian evolutionary analysis indicated that the ancestors of Irpicaceae and Steccherinaceae are estimated to have emerged with mean crown ages of 199.17 Mya and 142.95 Mya, respectively, followed by the genus Odentinium, with a mean crown age of 120.8 Mya
Comparative analysis on rhizosphere microorganisms of Cynodon dactylon (Poaceae) from the natural restoration area and eco-restoration engineering area in water-level-fluctuation zone of Jinsha River-type reservoirs, China
No full textRhizosphere microorganisms may play an important role in plant growth and environmental adaptation during eco-restoration engineering in the water-level-fluctuation zone (WLFZ) of large river-type reservoirs. The purpose of this study is to compare the rhizosphere microbial community features of Cynodon dactylon derived from the natural restoration area (NEE) and eco-restoration engineering area (YEE) in the WLFZ of Jinsha River-type reservoirs using high-throughput sequencing and bioinformatic analyses. The dominant taxa were Proteobacteria and Ascomycota in C. dactylon rhizosphere from both NEE and YEE. The eco-restoration engineering improved the α-diversity of bacterial community, but reduced the diversity of fungal community. Eco-restoration engineering did not change the dominant pattern of aerobic respiration I (cytochrome c) [PWY-3781] and aerobic respiration II (cytochrome c, yeast) [PWY-7279] metabolic pathways in the rhizosphere microbial community. Many microbes (such as Alphaproteobacteria and Sphingomonadaceae) in YEE were identified as significantly enriched biomarkers, while the key biomarkers in the rhizosphere in NEE are relatively limited where Burkholderiaceae and Burkholderiales may be the key characteristic microbe. Our study provides a theoretical basis and potential clue for understanding the role of eco-restoration engineering in the re-assembly of rhizosphere microorganisms and supporting vegetation restoration in the WLFZ of large river-type reservoirs
Saving European weatherfish, a swampy business
No full textOnce widespread in Flanders (northern part of Belgium), the European weatherfish (Misgurnus fossilis L., 1758) has been fading away since the 1950s and has reached a critically endangered status. To save this species from extinction, a Species Protection Plan was launched in 2021 focussing ona regional wide innovative eDNA survey,habitat restoration andgenetic strengthening of the relic populations by means of a captive breeding program financially supported by LIFE (B4B).Although a climate change induced shift in general water management - with attention for more ecologically driven river discharge dynamics (Eflows), rewetting and improving lateral connectivity - provides the right momentum, the road to recovery for this species remains bumpy. On the good side, the species distribution in Flanders seems a bit less dramatic since the eDNA campaign revealed 14 more relic populations, bringing the total currently to 23. Also the breeding program started to pay off with a production of ca. 100.000 individuals in 2025 and the first proof of subsequent natural reproduction in at least one population. On the other hand, classical fishery in most investigated relic populations had a very low success rate, potentially pointing to very low densities. Because of the high demand by different users for the little remaining open space, also habitat restoration remains very challenging in Flanders. Even within the nature conservation sector, the objectives are diverse and sometimes incompatible, leading to delays or even failure to initiate certain restoration projects. Last but not least, the settlement and spread of invasive oriental weatherfish species brings with it new threats and challenges. All the more reason to pool our knowledge and expertise at a European scale, for which SWAMP (Specialist Weatherfish Action and Monitoring Partnership) was recently established. Only by joining forces can we save this enigmatic species from fading further into oblivion (Suppl. material 1)
A comparative study of pelagic and benthic resource use by invasive gibel carp (Carassius gibelio) and native crucian carp (Carassius carassius)
No full textThe efficient exploitation of available food resources is important for the prosperity and survival of any species. It influences not only growth and reproduction, but also the competitiveness of a species in the ecosystem. The native crucian carp (Carassius carassius) is currently considered critically endangered in the Czech Republic, primarily due to competitive pressure from the invasive gibel carp (Carassius gibelio). The underlying mechanisms driving this strong interspecific interaction are still poorly understood. This study explores differences in pelagic and benthic foraging between these two species under contrasting environmental conditions (clear vs. turbid water), using controlled laboratory experiments. To identify species-specific differences in foraging efficiency as determined by prey type and size, we conducted manipulative predation experiments using model prey organisms consisting of two size classes of Daphnia galeata and larvae of Chironomus plumosus. The results demonstrated that gibel carp exhibited significantly higher prey capture rates than native crucian carp in both pelagic and benthic prey types, suggesting a greater potential to exploit and successfully utilize available food resources. The invasive gibel carp also displayed higher levels of activity and boldness, supporting its propensity for more aggressive exploitation of the environment. Such superior foraging efficiency of invasive gibel carp may be a major factor contributing to the decline of crucian carp populations in small water bodies where both species co-occur
The Phylogenetic Imperative: A Genetics-Informed Framework Delineating Conservation Units for Carassius carassius in Czechia
No full textThe conservation of declining wetland fish species in Central Europe necessitates a paradigm shift from species-level management to the preservation of evolutionarily significant phylogenetic lineages. The crucian carp (Carassius carassius) is a compelling case study of the challenges of modern conservation, where a species' apparent widespread distribution belies a complex, fragmented genetic structure. Within Europe, the species is not a monolithic entity but rather comprises two distinct and highly divergent phylogenetic lineages. The first, a northern lineage, is found across a vast expanse of Northern and Eastern Europe, including the Labe (Elbe) and Odra (Oder) River Basins. The second, a Danubian lineage, is geographically restricted to the Danube River Basin. Critically, both of these natural, evolutionarily distinct lineages are native to the Czech Republic, with some regions serving as a vital contact zone where their historical ranges overlap. The explicit recommendation to classify this Central European lineage as "critically endangered" and to prioritize its protection is a powerful argument for a new framework of conservation. It moves the discussion beyond simply asking, "Is the species endangered?" to a more nuanced question: "What specific, irreplaceable genetic units are at highest risk?" This approach elevates a population's conservation priority based not only on its vulnerability but also on the irreplaceability of its unique evolutionary history. This model is directly applicable to the conservation of C. carassius and other species with similar fragmented genetic structures. It suggests that policy and funding decisions should be guided by a species' unique evolutionary trajectory and the critical need to preserve its genetic subgroups as distinct ecological and evolutionary entities
Recent data on the fish fauna of the lower Cerna River (Danube River System) with special remarks on the first occurrence of Balkan Loach Cobitis elongata (Pisces, Teleostei, Cobitidae)
No full textThis paper presents the recent results of the fish faunal study carried out in the lower course of the Cerna River, between the confluence with its main tributary (Belareca River), and until its discharge into the Danube. The study was carried out between 2020–2024 and refers to four sampling stations. Nineteen fish species were identified, besides the first occurrence of Cobitis elongata – the Balkan loach. The first record of this species in Cerna River is an important discovery as long as the previous data, including fish surveys in the studied area, do not mention the species in this river system
Distribution and ecological preferences of Ovalona karelica (Stenroos, 1897) (Crustacea, Branchiopoda, Cladocera) in Volga River Basin (European Russia)
No full textThe distribution and ecological preferences of the rare water flea Ovalona karelica (Stenroos, 1897) (Crustacea, Branchiopoda, Cladocera) were analysed for the first time for European Russia. The species was found in different types of waterbodies, such as floodplain lakes of the Kerzhensky State Nature Biosphere Reserve, Nizhny Novgorod City and mouths of rivers inflowing into reservoirs. Ovalona karelica inhabits waters with wide ranges of pH, salinity, oxygen content and trophicity. Development of semi-submerged macrophytes (Stratiotes, Hydrocharis, Salvinia) is the main factor influencing occurrence of the species and its abundance
The genus Euphitrea Baly, 1875 (Coleoptera, Chrysomelidae, Galerucinae, Alticitae) in Taiwan, with description of three new species
No full textThree previously described species of Euphitrea from Taiwan are recognized and redescribed: E. flavicornis (Chen, 1933), E. nisotroides (Chen, 1933), and E. taiwana Kimoto, 1991. Additionally, three new species from Taiwan are described: E. tsoui sp. nov., E. houjayi sp. nov., and E. jungchani sp. nov. The species descriptions include illustrations of aedeagi, antennae, gonocoxae, abdominal ventrite VIII, and spermathecae. Lectotypes are designated for Neorthaea flavicornis Chen, 1933 and N. nisotroides Chen, 1933